[AMBER] Error: Sander output is missing values! VDWAALS = *************

From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Tue, 7 Dec 2010 13:21:46 +0900

Hello amber users,

I am running MMPBSA.py.MPI on trajectories obtained from MD simulation on a
complex which contained four ZN ions and two Cl- ions. I did not remove Cl-
before simulations. Can that be the reason why I am getting this error ? -

Starting pb calculation...

  calculating ligand contribution...
  calculating receptor contribution...
  calculating complex contribution...

Calculations complete. Writing output file(s)...
Error: Sander output is missing values!
VDWAALS = ************* EEL = -19824.2815 EPB = -4539.5565
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.

The output file has correct guess for ligand and receptor so I guess the
prmtop and trajectories are compatible. Could you please tell me how to
remove these Cl- ions from the trajectories before running MMPBSA.py (if Cl-
ions are the problem). I just did pb calculations (not gb because it was
saying 'bad atom type ZN')

Thank you
Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN
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Received on Mon Dec 06 2010 - 20:30:03 PST
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